Bachelors Thesis(Jun 2009)
Keywords: heterogeneity, evolutionary rate
Determining the evolutionary history of genes and organisms is a critical aspect of field as diverse as developmental biology, astrobiology, history, anthropology, and medicine. The understanding gained through these phylogenetic analyses provides valuable information about the past and present unavailable through other avenues. The most widely used modern phylogenetic techniques require some knowledge about how evolution works to ensure accurate results. Selecting the best evolutionary model available for a given set of data is thus a critical step of phylogenetic analyses. One aspect of evolution that is not commonly accounted for is when different sites on a sequence have varying rates of change that differ in location on the sequences being compared. This phenomena, known as heterotachy, has been shown to be modeled best by a Mixed Branch Length (MBL) model. The question then is how many heterotachous partitions are needed to be adequately model the underlying evolutionary history. This question is answered through the empirical evaluation of modern model selection techniques on simulated data. The findings suggest that the Akaike Information Criterion (AIC) is the best technique for determining the number of heterotachous rate partitions to use in the MBL Model of evolution.